[ccp4bb] Fast searching of articles related to your PubMed indexed paper

[Yaoqi Zhou]

Fast searching of articles related to your PubMed indexed paper  
Are you spending too much time searching the literature to prepare your grant 
proposals, manuscripts and keeping track of research happening in your field? 
We have built a literature-based search engine 
(http://pubmed.ict.griffith.edu.au/ ) which 
is powered by a combination of state-of-the-art methods to locate relevant 
articles to your published PubMed-indexed papers within a few seconds.

While providing you the ability to locate relevant articles, we are seeking 
your feedback regarding the performance of these algorithms. By annotating 
recommended articles as relevant, somewhat relevant, or irrelevant, you are 
participating in a community-wide effort of establishing a gold-standard 
benchmark for relevant literature search.

The accuracy of this benchmark is ensured by your domain knowledge and 
experience as your judgements will be based in the context of your own article. 
With your expertise, the entire process will take only a few minutes to 
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development of next-generation literature searching and retrieval 
methodologies, something we all desperately need.

Due to current data availability, this relevant-paper search is limited to 
papers indexed by PubMed between January 1, 2007 to December 31, 2016 (the end 
of last year). Click http://pubmed.ict.griffith.edu.au/ 
 to start. As this is a product in 
development, any constructive comments and suggestions will be truly 
appreciated.

If you like this idea of community-wide benchmark for literature 
recommendation, please forward this email to your colleagues in the scientific 
community.

Initial feedbacks to our server. “The process was certainly fast!”, “Although 
the articles found in the search were not necessarily exactly relevant, many 
are articles that I don't think I would have come across easily with a 
traditional search”, “Very nice work. I think there can be a longer list” 
(limited to 30 currently).
Thank you!

Yaoqi

Professor Yaoqi Zhou | Research Leader
Institute for Glycomics
Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics 
(G24) Room 2.10
T +61 7 5552 8228 | F +61 7 5552 9040 | email yaoqi.z...@griffith.edu.au 
 

http://sparks-lab.org  (Group webpage)

http://griffith.edu.au/institute-glycomics 
 (Institute Webpage)

> On 25 Jul 2017, at 9:01 AM, CCP4BB automatic digest system 
>  wrote:
> 
> There are 14 messages totaling 9878 lines in this issue.
> 
> Topics of the day:
> 
>  1. Buccaneer places residues in different asymmetric units (3)
>  2. Primer design (7)
>  3. PhD position at University of Oslo
>  4. Postdoctoral position at Boston Children’s Hospital
>  5. About weighting factor settings in new ccp4i2 (2)
> 
> --
> 
> Date:Mon, 24 Jul 2017 16:56:51 +0800
> From:Lingxiao Zeng 
> Subject: Buccaneer places residues in different asymmetric units
> 
> Dear All,
> 
> I tried to use buccaneer to build a model. The starting model is a partial 
> model, after model building the Rwork and Rfree are reasonable but buccaneer 
> places residues in different asymmetric units and the model looks really 
> weird.
> 
> Is there any way to build the model into the same ASU or put different parts 
> together after model building? Thanks!
> 
> 
> 
> Best,
> 
> Alice
> 
> --
> Lingxiao Zeng
> PhD candidate
> School of Biomedical Sciences
> The University of Hong Kong
> 
> --
> 
> Date:Mon, 24 Jul 2017 10:35:17 +0100
> From:Jon Agirre 
> Subject: Re: Buccaneer places residues in different asymmetric units
> 
> Dear Alice,
> 
> there's an option in both ccp4i and ccp4i2 interfaces that lets you tell
> Buccaneer that you want to build the new model in the same place as the
> partial model supplied - see my screenshots for reference. It might not be
> on by default and perhaps it should be.
> 
> Please be aware that most newer developments and improvements will be put
> on the ccp4i2 interface to Buccaneer - it would be helpful if you could
> have a go and let us know what you think!
> 
> Hope this helps,
> 
> Jon
> 
> On 24 July 2017 at 09:56, Lingxiao Zeng  wrote:
> 
>> Dear All,
>> 
>> 
>> I tried to use buccaneer to build a model. The starting model is a partial
>> model, after model building the Rwork and Rfree are reasonable but
>> buccaneer places residues in different asymmetric units and the model looks
>> really weird.
>> 
>> 
>> Is there any way to build the model into the same ASU or put different
>> parts 

Re: [ccp4bb] Chain ID number limit!

[Lijun Liu]

Thanks this must be a fix.  I tried once but the loading file within the 
window did not give an option of .ciff (only for restraints).  I will 
try again.



On 07/24/2017 05:24 PM, Pavel Afonine wrote:

Hi Lijun,

it's not a problem if you use mmCIF or PDB with two-letter chain ID 
(both supported in Phenix).


Pavel

On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu > wrote:


Hi:  this must be an old problem but I would like to know if there
are other ideas to make things easier.

I solved a structure that contains 240 helices of identical
sequences in the asymmetric unit.  Handling so many chains is
really a headache as pdb contains only a single column for chain
ID (currently support up to 61 chains).  I had to combine some
(say a tetramer) as a single chain for a trick, which made me use
just enough letters/numbers (A-Z,1-9,a-z).  However this will need
further manual dealing with OXTs (currently I cheat with single N
of a residue) and raise new problems (like restraints).  Some
softwares does even not recognize chain IDs like a-z.  SegID might
be another trick however nowadays many softwares won't take that
part, so a down-to-chain rigid body / TLS refinement could be
impossible, without the combination trick.

With tricks I am ok to make things going?  But is there a solution
really solve the many-chain problem with PDB?

Best,

Lijun



Sent from my iPhone

Re: [ccp4bb] Chain ID number limit!

[Pavel Afonine]

Hi Lijun,

it's not a problem if you use mmCIF or PDB with two-letter chain ID (both
supported in Phenix).

Pavel

On Mon, Jul 24, 2017 at 5:09 PM, Lijun Liu  wrote:

> Hi:  this must be an old problem but I would like to know if there are
> other ideas to make things easier.
>
> I solved a structure that contains 240 helices of identical sequences in
> the asymmetric unit.  Handling so many chains is really a headache as pdb
> contains only a single column for chain ID (currently support up to 61
> chains).  I had to combine some (say a tetramer) as a single chain for a
> trick, which made me use just enough letters/numbers (A-Z,1-9,a-z).
> However this will need further manual dealing with OXTs (currently I cheat
> with single N of a residue) and raise new problems (like restraints).  Some
> softwares does even not recognize chain IDs like a-z.  SegID might be
> another trick however nowadays many softwares won't take that part, so a
> down-to-chain rigid body / TLS refinement could be impossible, without the
> combination trick.
>
> With tricks I am ok to make things going?  But is there a solution really
> solve the many-chain problem with PDB?
>
> Best,
>
> Lijun
>
>
>
> Sent from my iPhone

[ccp4bb] Chain ID number limit!

[Lijun Liu]

Hi:  this must be an old problem but I would like to know if there are other 
ideas to make things easier.

I solved a structure that contains 240 helices of identical sequences in the 
asymmetric unit.  Handling so many chains is really a headache as pdb contains 
only a single column for chain ID (currently support up to 61 chains).  I had 
to combine some (say a tetramer) as a single chain for a trick, which made me 
use just enough letters/numbers (A-Z,1-9,a-z).  However this will need further 
manual dealing with OXTs (currently I cheat with single N of a residue) and 
raise new problems (like restraints).  Some softwares does even not recognize 
chain IDs like a-z.  SegID might be another trick however nowadays many 
softwares won't take that part, so a down-to-chain rigid body / TLS refinement 
could be impossible, without the combination trick.

With tricks I am ok to make things going?  But is there a solution really solve 
the many-chain problem with PDB?

Best,

Lijun



Sent from my iPhone

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

[Paul Emsley]

Here's a new(er) trick with Coot:

Centre on an atom in a symmetry-related molecule where you want your model 
chain to be

Extensions -> Modelling -> Symm Shift Reference Chain Here.

Paul.

On 25/07/2017 00:05, Diana Tomchick wrote:

Or use Coot to generate the symmetry mates, then write out the symmetry-related 
coordinates.

Many ways to achieve the same outcome,

Diana

On Jul 24, 2017, at 3:56 AM, Lingxiao Zeng > wrote:


Dear All,

I tried to use buccaneer to build a model. The starting model is a partial model, after 
model building the Rwork and Rfree are reasonable but buccaneer places residues in different 
asymmetric units and the model looks really weird.


Is there any way to build the model into the same ASU or put different parts together after 
model building? Thanks!




Best,

Alice

--
Lingxiao Zeng
PhD candidate
School of Biomedical Sciences
The University of Hong Kong





UTSouthwestern

Medical Center

The future of medicine, today.

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

[Diana Tomchick]

Or use Coot to generate the symmetry mates, then write out the symmetry-related 
coordinates.

Many ways to achieve the same outcome,

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Jul 24, 2017, at 3:56 AM, Lingxiao Zeng 
> wrote:

Dear All,

I tried to use buccaneer to build a model. The starting model is a partial 
model, after model building the Rwork and Rfree are reasonable but buccaneer 
places residues in different asymmetric units and the model looks really weird.

Is there any way to build the model into the same ASU or put different parts 
together after model building? Thanks!



Best,

Alice

--
Lingxiao Zeng
PhD candidate
School of Biomedical Sciences
The University of Hong Kong





UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] About weighting factor settings in new ccp4i2

[Jon Agirre]

Dear Xu,

you can input those keywords in the text box under 'Advanced options' in
the 'refinement' task. Just make sure you click somewhere else after you're
done putting the keywords in in order to have the text validated by the
interface.

Best regards,
Jon

On 24 July 2017 at 23:01, Liu, Xu  wrote:

> Hi,
>
> In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting factor
> for B factor restrain weight (the ‘WBSKAL' setting) and/or x-ray terms
> relative to geometric restrains  (the ‘MATRIX’ setting ) in refmac5?
> Basically I want to plug in those weighting factors from pdbredo into
> REFMAC5 for a few more refinement but cannot find in new ccp4.
>
> Thanks!
>
> 
>
> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
> recipient, you are hereby notified that any dissemination, distribution
> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
>



-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Twitter: @alwaysonthejazz
+44 (0) 1904 32 8270

[ccp4bb] About weighting factor settings in new ccp4i2

[Liu, Xu]

Hi,

In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting factor for B 
factor restrain weight (the ‘WBSKAL' setting) and/or x-ray terms relative to 
geometric restrains  (the ‘MATRIX’ setting ) in refmac5? Basically I want to 
plug in those weighting factors from pdbredo into REFMAC5 for a few more 
refinement but cannot find in new ccp4.

Thanks!



This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).

Re: [ccp4bb] Primer design

[Tom Peat]

A lot of plant genomes are big- wheat for example is 12 Gb, so it may not be 
quite as trivial as one might expect. 
cheers, tom

Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Keller, Jacob 

Sent: Tuesday, July 25, 2017 1:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Primer design

>No need of the whole exome. Sequencing The second PCR product will do the job 
>I guess. Second PCR (from the cDNA pool) with specific forward primer and and 
>oligodA reverse primer. Surely a matter of less than $3

$3 is a major understimation, but I see your point. On the other hand, it is 
important to consider new technologies, and it would be a service to the 
scientific community to publish the exome somewhere, so other researchers would 
not have to spend their $3.

JPK





Best,

DKG


- Original Message -
From: "Jacob Keller" 
To: "Debasish Kumar Ghosh" , CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 6:48:25 PM
Subject: RE: Primer design

Or sequence the whole exome for what, $500-1000?

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish 
Kumar Ghosh
Sent: Monday, July 24, 2017 7:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Primer design

Dear Syed,

The process is very trivial to clone your gene of interest. Assuming your gene 
is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse 
primer. First isolate the total RNA from the tissue or cells and do the cDNA 
synthesis using oligodT primer followed by gene specific PCR with forward 
primer and oligodA primer from the cDNA pool. Sequence the PCR product to get 
to know the first stop codon in the ORF. Making the specific reverse primer 
from the sequence is then just matter of time.
Hope this helps.

Best wishes,

Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group Centre for DNA Fingerprinting and 
Diagnostics Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: 
http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: "syed ibrahim" <048c02cac012-dmarc-requ...@jiscmail.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 4:56:00 PM
Subject: [ccp4bb] Primer design

Hello All

I am interested in cloning a gene from a plant. I searched the database only 
partial sequence is available, ie: for 160 residues only. The full length of 
the protein is around 570 residues. I designed forward primer and I have no 
clue to design reverse primer.

Any help

Thank you

Syed

[ccp4bb] Postdoctoral position at Boston Children’s Hospital

[Bing Chen]

A postdoctoral position is available immediately in Dr. Bing Chen’s 
laboratory at Boston Children’s Hospital/Harvard Medical School.


The ongoing projects include 1) biochemical and structural studies to 
elucidate molecular mechanisms of how HIV-1 enters host cells, 2) design 
and production of HIV-1 envelope-based immunogens, and 3) development of 
antiviral therapeutics.


For our recent publications, please see:

Cai et al., Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4477-4482.  
(https://www.ncbi.nlm.nih.gov/pubmed/28396421 
)


Dev et al., Science. 2016 Jul 8;353(6295):172-5. 
(https://www.ncbi.nlm.nih.gov/pubmed/27338706 
)


Chen et al., Science. 2015 Jul 10;349(6244):191-5. 
(https://www.ncbi.nlm.nih.gov/pubmed/26113642 
)


A strong background in protein biochemistry and/or structural biology is 
required. We are particularly interested in those who are highly 
motivated and willing to tackle difficult problems. Applicants should 
send a cover letter, CV, and contact information of three references to 
Bing Chen (bc...@crystal.harvard.edu ).

Re: [ccp4bb] Primer design

[Keller, Jacob]

>No need of the whole exome. Sequencing The second PCR product will do the job 
>I guess. Second PCR (from the cDNA pool) with specific forward primer and and 
>oligodA reverse primer. Surely a matter of less than $3 

$3 is a major understimation, but I see your point. On the other hand, it is 
important to consider new technologies, and it would be a service to the 
scientific community to publish the exome somewhere, so other researchers would 
not have to spend their $3.

JPK





Best,

DKG


- Original Message -
From: "Jacob Keller" 
To: "Debasish Kumar Ghosh" , CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 6:48:25 PM
Subject: RE: Primer design

Or sequence the whole exome for what, $500-1000?

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish 
Kumar Ghosh
Sent: Monday, July 24, 2017 7:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Primer design

Dear Syed,

The process is very trivial to clone your gene of interest. Assuming your gene 
is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse 
primer. First isolate the total RNA from the tissue or cells and do the cDNA 
synthesis using oligodT primer followed by gene specific PCR with forward 
primer and oligodA primer from the cDNA pool. Sequence the PCR product to get 
to know the first stop codon in the ORF. Making the specific reverse primer 
from the sequence is then just matter of time.  
Hope this helps.

Best wishes,

Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group Centre for DNA Fingerprinting and 
Diagnostics Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: 
http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: "syed ibrahim" <048c02cac012-dmarc-requ...@jiscmail.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 4:56:00 PM
Subject: [ccp4bb] Primer design

Hello All

I am interested in cloning a gene from a plant. I searched the database only 
partial sequence is available, ie: for 160 residues only. The full length of 
the protein is around 570 residues. I designed forward primer and I have no 
clue to design reverse primer.

Any help

Thank you

Syed

Re: [ccp4bb] Primer design

[Debasish Kumar Ghosh]

No need of the whole exome. Sequencing The second PCR product will do the job I 
guess. Second PCR (from the cDNA pool) with specific forward primer and and 
oligodA reverse primer. Surely a matter of less than $3 

Best,

DKG


- Original Message -
From: "Jacob Keller" 
To: "Debasish Kumar Ghosh" , CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 6:48:25 PM
Subject: RE: Primer design

Or sequence the whole exome for what, $500-1000?

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish 
Kumar Ghosh
Sent: Monday, July 24, 2017 7:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Primer design

Dear Syed,

The process is very trivial to clone your gene of interest. Assuming your gene 
is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse 
primer. First isolate the total RNA from the tissue or cells and do the cDNA 
synthesis using oligodT primer followed by gene specific PCR with forward 
primer and oligodA primer from the cDNA pool. Sequence the PCR product to get 
to know the first stop codon in the ORF. Making the specific reverse primer 
from the sequence is then just matter of time.  
Hope this helps.

Best wishes,

Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group Centre for DNA Fingerprinting and 
Diagnostics Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: 
http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: "syed ibrahim" <048c02cac012-dmarc-requ...@jiscmail.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 4:56:00 PM
Subject: [ccp4bb] Primer design

Hello All

I am interested in cloning a gene from a plant. I searched the database only 
partial sequence is available, ie: for 160 residues only. The full length of 
the protein is around 570 residues. I designed forward primer and I have no 
clue to design reverse primer.

Any help

Thank you

Syed

Re: [ccp4bb] Primer design

[Keller, Jacob]

Or sequence the whole exome for what, $500-1000?

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish 
Kumar Ghosh
Sent: Monday, July 24, 2017 7:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Primer design

Dear Syed,

The process is very trivial to clone your gene of interest. Assuming your gene 
is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse 
primer. First isolate the total RNA from the tissue or cells and do the cDNA 
synthesis using oligodT primer followed by gene specific PCR with forward 
primer and oligodT primer from the cDNA pool. Sequence the PCR product to get 
to know the first stop codon in the ORF. Making the specific reverse primer 
from the sequence is then just matter of time.  
Hope this helps.

Best wishes,

Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group Centre for DNA Fingerprinting and 
Diagnostics Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: 
http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: "syed ibrahim" <048c02cac012-dmarc-requ...@jiscmail.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 4:56:00 PM
Subject: [ccp4bb] Primer design

Hello All

I am interested in cloning a gene from a plant. I searched the database only 
partial sequence is available, ie: for 160 residues only. The full length of 
the protein is around 570 residues. I designed forward primer and I have no 
clue to design reverse primer.

Any help

Thank you

Syed

Re: [ccp4bb] Buccaneer places residues in different asymmetric units

[Eleanor Dodson]

Or use PISA to position bits sensibly..
Eleanor

On 24 July 2017 at 10:35, Jon Agirre  wrote:

> Dear Alice,
>
> there's an option in both ccp4i and ccp4i2 interfaces that lets you tell
> Buccaneer that you want to build the new model in the same place as the
> partial model supplied - see my screenshots for reference. It might not be
> on by default and perhaps it should be.
>
> Please be aware that most newer developments and improvements will be put
> on the ccp4i2 interface to Buccaneer - it would be helpful if you could
> have a go and let us know what you think!
>
> Hope this helps,
>
> Jon
>
> On 24 July 2017 at 09:56, Lingxiao Zeng  wrote:
>
>> Dear All,
>>
>>
>> I tried to use buccaneer to build a model. The starting model is a
>> partial model, after model building the Rwork and Rfree are reasonable but
>> buccaneer places residues in different asymmetric units and the model looks
>> really weird.
>>
>>
>> Is there any way to build the model into the same ASU or put different
>> parts together after model building? Thanks!
>>
>>
>>
>>
>> Best,
>>
>> Alice
>>
>> --
>> Lingxiao Zeng
>> PhD candidate
>> School of Biomedical Sciences
>> The University of Hong Kong
>>
>>
>
>
> --
> Dr Jon Agirre
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, England
> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
> Twitter: @alwaysonthejazz
> +44 (0) 1904 32 8270
>

Re: [ccp4bb] Primer design

[Debasish Kumar Ghosh]

Dear Syed,

The process is very trivial to clone your gene of interest. Assuming your gene 
is transcribed as mono-cistronic mRNA, take the oligodT primer as reverse 
primer. First isolate the total RNA from the tissue or cells and do the cDNA 
synthesis using oligodT primer followed by gene specific PCR with forward 
primer and oligodT primer from the cDNA pool. Sequence the PCR product to get 
to know the first stop codon in the ORF. Making the specific reverse primer 
from the sequence is then just matter of time.  
Hope this helps.

Best wishes,

Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: "syed ibrahim" <048c02cac012-dmarc-requ...@jiscmail.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, July 24, 2017 4:56:00 PM
Subject: [ccp4bb] Primer design

Hello All

I am interested in cloning a gene from a plant. I searched the database only 
partial sequence is available, ie: for 160 residues only. The full length of 
the protein is around 570 residues. I designed forward primer and I have no 
clue to design reverse primer.

Any help

Thank you

Syed

Re: [ccp4bb] Primer design

[Artem Evdokimov]

Have to do primer walking in a cdna library first.

Artem

On Jul 24, 2017 7:26 AM, "syed ibrahim" <
048c02cac012-dmarc-requ...@jiscmail.ac.uk> wrote:

Hello All

I am interested in cloning a gene from a plant. I searched the database
only partial sequence is available, ie: for 160 residues only. The full
length of the protein is around 570 residues. I designed forward primer and
I have no clue to design reverse primer.

Any help

Thank you

Syed

[ccp4bb] Primer design

[syed ibrahim]

Hello All

I am interested in cloning a gene from a plant. I searched the database only 
partial sequence is available, ie: for 160 residues only. The full length of 
the protein is around 570 residues. I designed forward primer and I have no 
clue to design reverse primer.

Any help

Thank you

Syed

[ccp4bb] Buccaneer places residues in different asymmetric units

[Lingxiao Zeng]

Dear All,

I tried to use buccaneer to build a model. The starting model is a partial 
model, after model building the Rwork and Rfree are reasonable but buccaneer 
places residues in different asymmetric units and the model looks really weird.

Is there any way to build the model into the same ASU or put different parts 
together after model building? Thanks!



Best,

Alice

--
Lingxiao Zeng
PhD candidate
School of Biomedical Sciences
The University of Hong Kong